scholarly journals Systematic identification and characterization of Aedes aegypti long noncoding RNAs

2018 ◽  
Author(s):  
Azali Azlan ◽  
Sattam M. Obeidat ◽  
Muhammad Amir Yunus ◽  
Ghows Azzam
Keyword(s):  
Aedes Aegypti ◽  
Early Stage ◽  
Developmental Regulation ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Transcriptional Response ◽  
Long Noncoding Rnas ◽  
Blood Sucking ◽  
Virus Serotype ◽  
Systematic Identification

Long noncoding RNAs (lncRNAs) play diverse roles in biological process including developmental regulation and host-pathogen interactions. Aedes aegypti (Ae. aegypti), a blood-sucking mosquito, is the principal vector responsible for replication and transmission of arboviruses including dengue, zika, and chikungunya virus. Systematic identification and developmental characterisation of Ae. aegypti lncRNAs are still limited. We performed genome-wide identification of lncRNAs followed by developmental profiling of lncRNA expression in Ae. aegypti. We identified a total of 4,689 novel lncRNA transcripts, of which 2,064, 2,076, and 549 were intergenic, intronic, and antisense respectively. Ae. aegypti lncRNAs shared many of the characteristics with other species including low expression, low GC content, short in length, low conservation, and their expression tended to be correlated with neighbouring and antisense protein-coding genes. Subsets of lncRNAs showed evidence that they were maternally inherited, suggesting potential roles in early-stage embryos. Additionally, lncRNAs showed higher tendency to be expressed in developmental and temporal specific manner. Upon infection of Ae. aegypti cells with dengue virus serotype 1, we identified 2,335 differentially expressed transcripts, 957 of which were lncRNA transcripts. The systematic annotation, developmental profiling, and transcriptional response upon virus infection provide foundation for future investigation on the function of Ae. aegypti lncRNAs.

scholarly journals Identification and characterization of long noncoding RNAs and their association with acquisition of blood meal in Culex quinquefasciatus

2020 ◽  
Author(s):  
Azali Azlan ◽  
Mardani Abdul Halim ◽  
Faisal Mohamad ◽  
Ghows Azzam
Keyword(s):  
Culex Quinquefasciatus ◽  
Blood Meal ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Blood Feeding ◽  
Long Noncoding Rnas ◽  
Host Interaction ◽  
Systematic Identification ◽  
Identification And Characterization

AbstractThe Southern house mosquito, Culex quinquefasciatus (Cx. quinquefasciatus) is an important vector that transmit multiple diseases including West Nile encephalitis, Japanese encephalitis, St. Louis encephalitis and lymphatic filariasis. Long noncoding RNAs (lncRNAs) involve in many biological processes such development, infection, and virus-host interaction. However, there is no systematic identification and characterization of lncRNAs in Cx. quinquefasciatus. Here, we report the first ever lncRNA identification in Cx. quinquefasciatus. By using 31 public RNA-seq datasets, a total of 4,763 novel lncRNA transcripts were identified, of which 3,591, 569, and 603 were intergenic, intronic, and antisense respectively. Examination of genomic features revealed that Cx. quinquefasciatus shared similar characteristics with other species such as short in length, low GC content, low sequence conservation, and low coding potential. Furthermore, compared to protein-coding genes, Cx. quinquefasciatus lncRNAs had lower expression values, and tended to be expressed in temporally-specific fashion. In addition, weighted correlation network and functional annotation analyses showed that lncRNAs may have roles in blood meal acquisition of adult female Cx. quinquefasciatus mosquitoes. This study presents the first systematic identification and analysis of Cx. quinquefasciatus lncRNAs and their association with blood feeding. Results generated from this study will facilitate future investigation on the function of Cx. quinquefasciatus lncRNAs.

scholarly journals Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Yalan Yang ◽  
Rong Zhou ◽  
Shiyun Zhu ◽  
Xunbi Li ◽  
Hua Li ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Long Noncoding Rnas ◽  
Molecular Characteristics ◽  
Characteristic Analysis ◽  
Bioinformatics Pipeline ◽  
Protein Coding ◽  
A Genome ◽  
Systematic Identification

Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs that are involved in a variety of biological processes. The pig is an important farm animal and an ideal biomedical model. In this study, we performed a genome-wide scan for lncRNAs in multiple tissue types from pigs. A total of 118 million paired-end 90 nt clean reads were obtained via strand-specific RNA sequencing, 80.4% of which were aligned to the pig reference genome. We developed a stringent bioinformatics pipeline to identify 2,139 high-quality multiexonic lncRNAs. The characteristic analysis revealed that the novel lncRNAs showed relatively shorter transcript length, fewer exons, and lower expression levels in comparison with protein-coding genes (PCGs). The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs. Moreover, the single nucleotide polymorphism (SNP) density of lncRNAs was significantly higher than that of PCGs. Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA MALAT1. The findings of our study significantly increase the number of known lncRNAs in pigs.

scholarly journals Systematic Identification of Long Noncoding RNAs in Immature and Mature Porcine Testes1

2016 ◽  
Vol 94 (4) ◽  
Author(s):  
Maoliang Ran ◽  
Bin Chen ◽  
Zhi Li ◽  
Maisheng Wu ◽  
Xiaochun Liu ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Systematic Identification

Abstract 91: Genome-wide Identification and Characterization of Cardiac Hypertrophy-related Long Noncoding RNAs in Mice

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Zhanpeng Huang ◽  
Gengze Wu ◽  
Jian-Hua Yang ◽  
Jian Ding ◽  
Jinghai Chen ◽  
...  
Keyword(s):  
Cardiac Hypertrophy ◽  
Target Genes ◽  
Troponin T ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Functional Screening ◽  
Loss Of Function ◽  
Specific Expression ◽  
Functional Conservation ◽  
Virus Serotype

Long noncoding RNAs (LncRNAs) are RNA transcripts longer than 200 nucleotides that lack protein-coding potential. Although thousands of lncRNAs have been identified, only a few have been linked to cardiac gene expression and function. In this study, we identified, from genome-scale RNA-seq data, 12 candidate lncRNAs associated with cardiac hypertrophy (CH-lncRNAs). The expression of these lncRNAs was altered in mouse models of cardiac hypertrophy induced by transverse aortic constriction (TAC)- or CnA transgene. To determine the function of these lncRNAs, we developed an adeno-associated virus serotype 9 (AAV9)-based functional screening in postnatal mice. An AAV9:cTNT vector, in which the cardiac troponin T (cTNT) promoter was used to direct cardiac-specific expression of target genes, was utilized to overexpress or knockdown candidate lncRNAs in mouse hearts. Postnatal day 1 wild type or CnA transgenic pups were injected with AAV9 viruses and cardiac function was measured one and two months later. Thus far, we have tested 15 candidate lncRNAs for both gain- and loss-of-function studies. Among them, two lncRNAs were demonstrated regulating hypertrophy growth when knocked down. Finally, we identified the human homologues of CH-lncRNA through analyzing the conservation of the promoter regions of lncRNA genes. We showed that the expression of these human CH-lncRNA was dysregulated in human diseased hearts, suggesting the functional conservation of these lncRNAs in cardiac disease. Our study therefore demonstrated that lncRNAs are important regulator of cardiac hypertrophy and disease.

scholarly journals Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and Zika virus infection

2021 ◽  
Vol 15 (1) ◽  
pp. e0008351
Author(s):  
Azali Azlan ◽  
Sattam M. Obeidat ◽  
Kumitaa Theva Das ◽  
Muhammad Amir Yunus ◽  
Ghows Azzam
Keyword(s):  
Virus Infection ◽  
Aedes Albopictus ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Target Prediction ◽  
Long Noncoding Rnas ◽  
Lncrna Transcript ◽  
Expression Of Genes ◽  
Asian Tiger ◽  
Public Datasets

The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). Long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae. albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus, and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae. albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutations in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus.

scholarly journals The p53 transcriptional response across tumor types reveals core and senescence-specific signatures modulated by long noncoding RNAs

2021 ◽  
Vol 118 (31) ◽  
pp. e2025539118
Author(s):  
Ephrath Tesfaye ◽  
Elena Martinez-Terroba ◽  
Jordan Bendor ◽  
Lauren Winkler ◽  
Christiane Olivero ◽  
...  
Keyword(s):  
Target Genes ◽  
Noncoding Rnas ◽  
Transcriptional Response ◽  
Long Noncoding Rnas ◽  
Tumor Type ◽  
Cycle Arrest ◽  
Permanent Cell ◽  
Suppressor Mechanism ◽  
Functional Investigation ◽  
Tumor Types

The p53 pathway is a universal tumor suppressor mechanism that limits tumor progression by triggering apoptosis or permanent cell cycle arrest, called senescence. In recent years, efforts to reactivate p53 function in cancer have proven to be a successful therapeutic strategy in murine models and have gained traction with the development of a range of small molecules targeting mutant p53. However, knowledge of the downstream mediators of p53 reactivation in different oncogenic contexts has been limited. Here, we utilized a panel of murine cancer cell lines from three distinct tumor types susceptible to alternative outcomes following p53 restoration to define unique and shared p53 transcriptional signatures. While we found that the majority of p53-bound sites and p53-responsive transcripts are tumor-type specific, analysis of shared targets identified a core signature of genes activated by p53 across all contexts. Furthermore, we identified repression of E2F and Myc target genes as a key feature of senescence. Characterization of p53-induced transcripts revealed core and senescence-specific long noncoding RNAs (lncRNAs) that are predominantly chromatin associated and whose production is coupled to cis-regulatory activities. Functional investigation of the contributions of p53-induced lncRNAs to p53-dependent outcomes highlighted Pvt1b, the p53-dependent isoform of Pvt1, as a mediator of p53-dependent senescence via Myc repression. Inhibition of Pvt1b led to decreased activation of senescence markers and increased levels of markers of proliferation. These findings shed light on the core and outcome-specific p53 restoration signatures across different oncogenic contexts and underscore the key role of the p53-Pvt1b-Myc regulatory axis in mediating proliferative arrest.

scholarly journals Analysis of Long Noncoding RNAs in Aila-Induced Non-Small Cell Lung Cancer Inhibition

2021 ◽  
Vol 11 ◽  
Author(s):  
Lin Chen ◽  
Cui Wu ◽  
Heming Wang ◽  
Sinuo Chen ◽  
Danhui Ma ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Early Stage ◽  
Noncoding Rnas ◽  
Small Cell ◽  
Long Noncoding Rnas ◽  
Dependent Manner ◽  
Small Cell Lung ◽  
Cancer Inhibition

Non-small cell lung cancer (NSCLC) has the highest morbidity and mortality among all carcinomas. However, it is difficult to diagnose in the early stage, and current therapeutic efficacy is not ideal. Although numerous studies have revealed that Ailanthone (Aila), a natural product, can inhibit multiple cancers by reducing cell proliferation and invasion and inducing apoptosis, the mechanism by which Aila represses NSCLC progression in a time-dependent manner remains unclear. In this study, we observed that most long noncoding RNAs (lncRNAs) were either notably up- or downregulated in NSCLC cells after treatment with Aila. Moreover, alterations in lncRNA expression induced by Aila were crucial for the initiation and metastasis of NSCLC. Furthermore, in our research, expression of DUXAP8 was significantly downregulated in NSCLC cells after treatment with Aila and regulated expression levels of EGR1. In conclusion, our findings demonstrate that Aila is a potent natural suppressor of NSCLC by modulating expression of DUXAP8 and EGR1.

scholarly journals Distribution, Characteristics, and Regulatory Potential of Long Noncoding RNAs in Brown-Rot Fungi

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Alessandra Borgognone ◽  
Walter Sanseverino ◽  
Riccardo Aiese Cigliano ◽  
Raúl Castanera
Keyword(s):  
Noncoding Rnas ◽  
Gc Content ◽  
Brown Rot ◽  
Long Noncoding Rnas ◽  
Upstream Gene ◽  
Coniophora Puteana ◽  
Brown Rot Fungi ◽  
Serpula Lacrymans ◽  
Genomic Regions

Long noncoding RNAs have been thoroughly studied in plants, animals, and yeasts, where they play important roles as regulators of transcription. Nevertheless, almost nothing is known about their presence and characteristics in filamentous fungi, especially in basidiomycetes. In the present study, we have carried out an exhaustive annotation and characterization of lncRNAs in two lignin degrader basidiomycetes, Coniophora puteana and Serpula lacrymans. We identified 2,712 putative lncRNAs in the former and 2,242 in the latter, mainly originating from intergenic locations of transposon-sparse genomic regions. The lncRNA length, GC content, expression levels, and stability of the secondary structure differ from coding transcripts but are similar in these two species and resemble that of other eukaryotes. Nevertheless, they lack sequence conservation. Also, we found that lncRNAs are transcriptionally regulated in the same proportion as genes when the fungus actively decomposes soil organic matter. Finally, up to 7% of the upstream gene regions of Coniophora puteana and Serpula lacrymans are transcribed and produce lncRNAs. The study of expression trends in these gene-lncRNA pairs uncovered groups with similar and opposite transcriptional profiles which may be the result of cis-transcriptional regulation.

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